""" uniqueify.py: CCP4 GUI Project Copyright (C) 2011 STFC Author: Martyn Winn This is modelled on the old unix script """ import os,shutil from CCP4PluginScript import CPluginScript class uniqueify(CPluginScript): TASKMODULE = 'test' # Where this plugin will appear on the gui TASKTITLE = 'Standardise reflection data file' # Short title for gui menu TASKNAME = 'uniqueify' # Task name - should be same as class name TASKVERSION= 0.0 # Version of this plugin def process(self): # Run mtzheader to get spg, cell, reso print "### Running mtzheader ###" unsetData = self.checkInputData() if len(unsetData)>0: self.reportStatus(CPluginScript.FAILED) return self.mtzheader = self.makePluginObject('mtzheader') self.mtzheader.container.inputData.HKLIN = self.container.inputData.HKLIN self.connectSignal(self.mtzheader,'finished',self.process_unique) self.mtzheader.process() def process_unique(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return ### determine workflow if self.container.controlParameters.COMPLETE == "Yes": self.route = "cad_copy_column" elif self.container.controlParameters.COMPLETE == "No": self.route = "freerflag" elif self.container.controlParameters.COMPLETE == "Auto": print "Auto not implemented yet" self.reportStatus(CPluginScript.FAILED) return print "### Running unique ###" # Run unique to get full list of reflections self.unique = self.makePluginObject('unique') self.unique.container.inputData.SPACEGROUPCELL = self.mtzheader.container.outputData.SPACEGROUPCELL self.unique.container.inputData.RESOLUTION = self.mtzheader.container.outputData.MAXRESOLUTION if self.route == "freerflag": self.connectSignal(self.unique,'finished',self.process_freerflag) if self.route == "cad_copy_column": self.connectSignal(self.unique,'finished',self.process_cad2) self.unique.process() def process_freerflag(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return print "### Running freerflag ###" # Run freerflag to attach freeR column self.freerflag = self.makePluginObject('freerflag') self.freerflag.container.inputData.HKLIN = self.unique.container.outputData.HKLOUT self.connectSignal(self.freerflag,'finished',self.process_cad) self.freerflag.process() def process_cad(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return print "### Running cad_copy_column ###" # Run cad to attach freeR column to original file self.cad_copy_column = self.makePluginObject('cad_copy_column') self.cad_copy_column.container.inputData.HKLIN1 = self.container.inputData.HKLIN self.cad_copy_column.container.inputData.HKLIN2 = self.freerflag.container.outputData.HKLOUT # for the moment, we assume freerflag has outputted standard label self.cad_copy_column.container.inputData.FREERFLAG.FREE = 'FreeR_flag' self.connectSignal(self.cad_copy_column,'finished',self.process_freerflag_tidy) self.cad_copy_column.process() def process_freerflag_tidy(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return print "### Running freerflag ###" # Run freerflag to ensure freeR column is complete # (experience shows that uniqueify can miss some reflections # on resolution limit) self.freerflag_tidy = self.makePluginObject('freerflag') self.freerflag_tidy.container.inputData.HKLIN = self.cad_copy_column.container.outputData.HKLOUT self.freerflag_tidy.container.inputData.FREERFLAG.FREE = 'FreeR_flag' self.freerflag_tidy.container.controlParameters.COMPLETE = True self.connectSignal(self.freerflag_tidy,'finished',self.process_finish) self.freerflag_tidy.process() def process_cad2(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return print "### Running cad_copy_column ###" # Run cad to attach unique columns to original file self.cad_copy_column2 = self.makePluginObject('cad_copy_column') self.cad_copy_column2.container.inputData.HKLIN1 = self.container.inputData.HKLIN self.cad_copy_column2.container.inputData.HKLIN2 = self.unique.container.outputData.HKLOUT # for the moment, we assume unique has outputted standard label self.cad_copy_column2.container.inputData.FSIGF.F = 'F' self.cad_copy_column2.container.inputData.FSIGF.SIGF = 'SIGF' self.connectSignal(self.cad_copy_column2,'finished',self.process_freerflag2) self.cad_copy_column2.process() def process_freerflag2(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return print "### Running freerflag ###" # Run freerflag to ensure freeR column is complete self.freerflag2 = self.makePluginObject('freerflag') self.freerflag2.container.inputData.HKLIN = self.cad_copy_column2.container.outputData.HKLOUT self.freerflag2.container.inputData.FREERFLAG.FREE = 'FreeR_flag' self.freerflag2.container.controlParameters.COMPLETE = True self.connectSignal(self.freerflag2,'finished',self.process_mtzutils) self.freerflag2.process() def process_mtzutils(self,status): if status.get('finishStatus') == CPluginScript.FAILED: self.reportStatus(status) return print "### Running mtzutils ###" # Run mtzutils to delete spurious columns self.mtzutils = self.makePluginObject('mtzutils') self.mtzutils.container.inputData.HKLIN1 = self.freerflag2.container.outputData.HKLOUT self.mtzutils.container.inputData.FSIGF.F = 'F' self.mtzutils.container.inputData.FSIGF.SIGF = 'SIGF' self.mtzutils.container.controlParameters.MODE = 'EXCLUDE' self.connectSignal(self.mtzutils,'finished',self.process_finish) self.mtzutils.process() def process_finish(self,status): if self.route == "freerflag": shutil.copyfile(str(self.freerflag_tidy.container.outputData.HKLOUT),str(self.container.outputData.HKLOUT)) if self.route == "cad_copy_column": shutil.copyfile(str(self.mtzutils.container.outputData.HKLOUT),str(self.container.outputData.HKLOUT)) # Emit finished signal with whatever status has been emitted # by the previous wrapper self.reportStatus(status.get('finshStatus')) #====================================================== # PLUGIN TESTS # See Python documentation on unittest module import unittest class testuniqueify(unittest.TestCase): def setUp(self): import CCP4Modules self.app = CCP4Modules.QTAPPLICATION() # make all background jobs wait for completion # this is essential for unittest to work CCP4Modules.PROCESSMANAGER().setWaitForFinished(10000) def tearDown(self): import CCP4Modules CCP4Modules.PROCESSMANAGER().setWaitForFinished(-1) def test_1(self): import CCP4Modules, CCP4Utils, os workDirectory = CCP4Utils.getTestTmpDir() # this needs to agree with name attribute below logFile = os.path.join(workDirectory,'uniqueify_test1.log') # Delete any existing log file if os.path.exists(logFile): os.remove(logFile) self.wrapper = uniqueify(parent=CCP4Modules.QTAPPLICATION(),name='uniqueify_test1',workDirectory=workDirectory) self.wrapper.container.loadDataFromXml(os.path.join(CCP4Utils.getCCP4I2Dir(),'pipelines','uniqueify','test_data','test1.data.xml')) self.wrapper.setWaitForFinished(1000000) pid = self.wrapper.process() self.wrapper.setWaitForFinished(-1) if len(self.wrapper.errorReport)>0: print self.wrapper.errorReport.report() #self.assertTrue(os.path.exists(logFile),'No log file found') def TESTSUITE(): suite = unittest.TestLoader().loadTestsFromTestCase(testuniqueify) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite)